TY  - JOUR
A1  - Kudron, Michelle
A1  - Gevirtzman, Louis
A1  - Victorsen, Alec
A1  - Lear, Bridget C.
A1  - Gao, Jiahao
A1  - Xu, Jinrui
A1  - Samanta, Swapna
A1  - Frink, Emily
A1  - Tran-Pearson, Adri
A1  - Huynh, Chau
A1  - Vafeados, Dionne
A1  - Hammonds, Ann
A1  - Fisher, William
A1  - Wall, Martha
A1  - Wesseling, Greg
A1  - Hernandez, Vanessa
A1  - Lin, Zhichun
A1  - Kasparian, Mary
A1  - White, Kevin
A1  - Allada, Ravi
A1  - Gerstein, Mark
A1  - Hillier, LaDeana
A1  - Celniker, Susan E.
A1  - Reinke, Valerie
A1  - Waterston, Robert H.
T1  - Binding profiles for 961 Drosophila and C. elegans transcription factors reveal tissue-specific regulatory relationships
Y1  - 2024/12/01 
JF  - Genome Research 
JO  - Genome Research 
SP  - 2319 
EP  - 2334 
DO  - 10.1101/gr.279037.124 
VL  - 34 
IS  - 12 
UR  - http://genome.cshlp.org/content/34/12/2319.abstract 
N2  - A catalog of transcription factor (TF) binding sites in the genome is critical for deciphering regulatory relationships. Here, we present the culmination of the efforts of the modENCODE (model organism Encyclopedia of DNA Elements) and modERN (model organism Encyclopedia of Regulatory Networks) consortia to systematically assay TF binding events in vivo in two major model organisms, Drosophila melanogaster (fly) and Caenorhabditis elegans (worm). These data sets comprise 605 TFs identifying 3.6 M sites in the fly and 356 TFs identifying 0.9 M sites in the worm, and represent the majority of the regulatory space in each genome. We demonstrate that TFs associate with chromatin in clusters termed “metapeaks,” that larger metapeaks have characteristics of high-occupancy target (HOT) regions, and that the importance of consensus sequence motifs bound by TFs depends on metapeak size and complexity. Combining ChIP-seq data with single-cell RNA-seq data in a machine-learning model identifies TFs with a prominent role in promoting target gene expression in specific cell types, even differentiating between parent–daughter cells during embryogenesis. These data are a rich resource for the community that should fuel and guide future investigations into TF function. To facilitate data accessibility and utility, all strains expressing green fluorescent protein (GFP)-tagged TFs are available at the stock centers for each organism. The chromatin immunoprecipitation sequencing data are available through the ENCODE Data Coordinating Center, GEO, and through a direct interface that provides rapid access to processed data sets and summary analyses, as well as widgets to probe the cell-type-specific TF–target relationships. 
ER  -